Hypothetically, science proves free will isn't real

[Angrboda]

It would seem that the mental abilities of humans serve well-enough the way we live. So do those of wasps, frogs, and horses. The question is whether reasoning is an advanced form of instinct or a different kind of thinking altogether.  I believe it is because 1) instinctual reactions seem directly related to the physical environment of organisms, including Man, whereas the referents of reasoning are abstracted concepts and 2) concepts have positive ontological status.

Weren't you the one who quoted Aquinas that there is nothing in the mind which doesn't first appear in the senses? You seem to be shifting your argument. Regardless, I don't believe that conceptual thinking is a special form of thinking. All our thoughts are essentially abstractions of our environment. It's possible that humans are alone in being able to do things like think of hypothetical futures and such, but there is nothing in any of this which implies it is more advanced than the thinking of animals. On top of that, unreason is built into the basement of reason. We have abstract thoughts to solve concrete puzzles, like how to get food and how to survive. These are the driving force of reason. “If everything on earth were rational, nothing would happen.” ~ Dostoyevsky

This is not to say that the realist position is without problems (which I feel can be resolved). Rather, that as a theory it explains more of the relevant phenomena than competing positions that have their own problems (which I find intractable).

Everyone always thinks this about the other guy.

And they don't necessarily not correspond to the way things are.  The proof is in the pudding.  In some ways the mind and perception can accurately model reality, in other ways, our biases, it does not.  

Since the pragmatic approach to everyday living and even natural science works, I also say go with it - methogologically. At the same time, you’re avoiding the question of whether it is possible for reason to overcome natural biases when dealing with ultimate issues. If it cannot then rationality has limits that prevent justification of everyday and scientific observations and there’s no way to know how far down that rabbit hole goes or accounting for the arbitrary point at which you stop trusting reason.

Your realism doesn't provide a stop for that any more than does skepticism. No it is not possible for reason to overcome its limits no matter what your existential commitment. As I've pointed out before, realism about the world doesn't lead to things-as-they-are, it just leads to models of what things-as-they-are is believed to be. But there is no way to tell if we are or are not at the last layer of the onion. It could go on further for all we know. Your commitments don't resolve that quandary. Reason, ultimately, cannot provide justification for itself. Your realism is no way out either.

… if we play on the other side of the fence, postulating that a perfectly rational superbeing imbued us and the universe with intelligibility doesn't get around the skeptical objections either.  Ultimately there's no justifiable reason for suspecting that an ultimate being isn't deceiving us about things-as-they-are.  It's no less an arbitrary assumption than is supposing that reason which comports with things-as-they-are has some sort of evolutionary value.

The existence of God is not my starting premise. My starting points are 1) the universe is intelligible and 2) human reason is effective. I freely acknowledge that those are existential commitments. I think knowledge of God’s existence follows from those commitments and reliable observations about reality. Skeptics make different existential commitments. Those commitments undermine the arguments for the existence of God. Those same commitments, as they relate to philosophical questions, come at great cost. They lead to paradoxes that undermine the veracity of reason or make ultimate reality absurd. That is the essence of my reply to the OP. Sure, determinism undermines many religious doctrines but in so doing it throws the baby out with the bathwater.

Even if I were to grant that your realism solves its problems, adopting an arbitrary response to these paradoxes is not doing philosophy, either. It's just a shortcut to a desired answer. The paradoxes are questions to be answered. This is not a bad result. Only the fool thinks he has it all figured out by merely avoiding the mysterious. Anyway, your argument that these paradoxes and seeming absurdities are a problem is at heart an argument from ignorance. We don't have the answers, therefore there is something wrong with the position. This kind of thinking characterizes all your attacks on atheism and skepticism. We don't have closure on the question of induction, therefore atheism is irrational for its dependence on science. We don't have an out from the regress of skepticism, therefore the position is flawed. It's a common theme in your thinking. And it's a fallacious way to reason about the subjects.